##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R version 4.6.0 alpha (2026-04-05 r89794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-04-08 07:29:29 UTC
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
               user system elapsed
dataHub-class 6.058  0.358   6.419
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘ReUseData’ ...
** this is package ‘ReUseData’ version ‘1.11.0’
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ReUseData)

R version 4.6.0 alpha (2026-04-05 r89794)
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(ReUseData)
> 
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)

}INFO Final process status is success

Updating data record...
outfile.txt added

Updating data record...
1477c744628a7c_GRCh38.primary_assembly.genome.fa.1.bt2 added
1477c730afcd1b_GRCh38.primary_assembly.genome.fa.2.bt2 added
1477c7d3a1618_GRCh38.primary_assembly.genome.fa.3.bt2 added
1477c76e5cfc9d_GRCh38.primary_assembly.genome.fa.4.bt2 added
1477c74b6e6a9f_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
1477c731ddb610_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
1477c72774014f_outfile.txt added
1477c76bc71f68_GRCh37_to_GRCh38.chain added
1477c74b36f4c0_GRCh37_to_NCBI34.chain added
1477c7315be7e8_GRCh37_to_NCBI35.chain added
1477c71396916b_GRCh37_to_NCBI36.chain added
1477c74d491d79_GRCh38_to_GRCh37.chain added
1477c71aca3a19_GRCh38_to_NCBI34.chain added
1477c7741acdd1_GRCh38_to_NCBI35.chain added
1477c779236ac7_GRCh38_to_NCBI36.chain added
1477c71fcb6051_NCBI34_to_GRCh37.chain added
1477c771ea1d2b_NCBI34_to_GRCh38.chain added
1477c7a7c78c3_NCBI35_to_GRCh37.chain added
1477c7407262d3_NCBI35_to_GRCh38.chain added
1477c74824b876_NCBI36_to_GRCh37.chain added
1477c74653c8bc_NCBI36_to_GRCh38.chain added
1477c77b4145f7_GRCm38_to_NCBIM36.chain added
1477c74b83e4ea_GRCm38_to_NCBIM37.chain added
1477c742a0179d_NCBIM36_to_GRCm38.chain added
1477c7273d0d27_NCBIM37_to_GRCm38.chain added
1477c728f58146_1000G_omni2.5.b37.vcf.gz added
1477c76af70202_1000G_omni2.5.b37.vcf.gz.tbi added
1477c7874fe99_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
1477c761f84592_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
1477c76c77660e_1000G_omni2.5.hg38.vcf.gz added
1477c715e65e5c_1000G_omni2.5.hg38.vcf.gz.tbi added
1477c7265ad00e_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
1477c71d27332a_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
1477c723207474_af-only-gnomad.raw.sites.vcf added
1477c714b7ccab_af-only-gnomad.raw.sites.vcf.idx added
1477c768959dc9_Mutect2-exome-panel.vcf.idx added
1477c754fe2a85_Mutect2-WGS-panel-b37.vcf added
1477c73c2bcdfa_Mutect2-WGS-panel-b37.vcf.idx added
1477c7545cbd32_small_exac_common_3.vcf added
1477c720351f45_small_exac_common_3.vcf.idx added
1477c76d87b5e2_1000g_pon.hg38.vcf.gz added
1477c767f34e9d_1000g_pon.hg38.vcf.gz.tbi added
1477c76d7e3cbe_af-only-gnomad.hg38.vcf.gz added
1477c7851effb_af-only-gnomad.hg38.vcf.gz.tbi added
1477c75c0e1c6e_small_exac_common_3.hg38.vcf.gz added
1477c766a1a785_small_exac_common_3.hg38.vcf.gz.tbi added
1477c7281d504d_gencode.v41.annotation.gtf added
1477c74df83999_gencode.v42.annotation.gtf added
1477c7711e2048_gencode.vM30.annotation.gtf added
1477c7688fb320_gencode.vM31.annotation.gtf added
1477c7161cf210_gencode.v41.transcripts.fa added
1477c73771e904_gencode.v41.transcripts.fa.fai added
1477c763d0f917_gencode.v42.transcripts.fa added
1477c761a0d6fa_gencode.v42.transcripts.fa.fai added
1477c77a1200a1_gencode.vM30.pc_transcripts.fa added
1477c7b0e063f_gencode.vM30.pc_transcripts.fa.fai added
1477c7a965840_gencode.vM31.pc_transcripts.fa added
1477c7650902a4_gencode.vM31.pc_transcripts.fa.fai added
1477c7138304d8_GRCh38.primary_assembly.genome.fa.1.ht2 added
1477c76c8e9dd2_GRCh38.primary_assembly.genome.fa.2.ht2 added
1477c7518068b2_GRCh38.primary_assembly.genome.fa.3.ht2 added
1477c729696334_GRCh38.primary_assembly.genome.fa.4.ht2 added
1477c712e96de1_GRCh38.primary_assembly.genome.fa.5.ht2 added
1477c76ea79bdc_GRCh38.primary_assembly.genome.fa.6.ht2 added
1477c74c89d7a9_GRCh38.primary_assembly.genome.fa.7.ht2 added
1477c727a13a8c_GRCh38.primary_assembly.genome.fa.8.ht2 added
1477c7573d39a6_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
1477c72188022e_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
1477c763cd0887_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
1477c72b99f6d8_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
1477c741bd2173_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
1477c75154be69_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
1477c7138d4575_GRCh38_full_analysis_set_plus_decoy_hla.fa added
1477c72f3b5e31_GRCh38.primary_assembly.genome.fa.fai added
1477c759a6ae65_GRCh38.primary_assembly.genome.fa.amb added
1477c76f9b61e3_GRCh38.primary_assembly.genome.fa.ann added
1477c715dd05b7_GRCh38.primary_assembly.genome.fa.bwt added
1477c71c3feb2_GRCh38.primary_assembly.genome.fa.pac added
1477c73d939b7d_GRCh38.primary_assembly.genome.fa.sa added
1477c76fb25ff_GRCh38.primary_assembly.genome.fa added
1477c76a53b1d2_hs37d5.fa.fai added
1477c753b08d8d_hs37d5.fa.amb added
1477c73e6d0f04_hs37d5.fa.ann added
1477c74e24aaea_hs37d5.fa.bwt added
1477c735516487_hs37d5.fa.pac added
1477c7387f0fa5_hs37d5.fa.sa added
1477c75932b129_hs37d5.fa added
1477c73fe7bcc8_complete_ref_lens.bin added
1477c71d881249_ctable.bin added
1477c76cb5b601_ctg_offsets.bin added
1477c72c765a9a_duplicate_clusters.tsv added
1477c76f087afc_info.json added
1477c7161f1936_mphf.bin added
1477c73f5fc87b_pos.bin added
1477c75db016d8_pre_indexing.log added
1477c762a8f0df_rank.bin added
1477c767010308_ref_indexing.log added
1477c734ed507e_refAccumLengths.bin added
1477c7430f30d_reflengths.bin added
1477c74ace0b8f_refseq.bin added
1477c760874756_seq.bin added
1477c745ee1480_versionInfo.json added
1477c71c22c9f8_salmon_index added
1477c774148ccb_chrLength.txt added
1477c7752972b1_chrName.txt added
1477c775c9785d_chrNameLength.txt added
1477c763afeeaf_chrStart.txt added
1477c7b067868_exonGeTrInfo.tab added
1477c7778d770f_exonInfo.tab added
1477c721438a2c_geneInfo.tab added
1477c712019e68_Genome added
1477c761e128e2_genomeParameters.txt added
1477c774f417b9_Log.out added
1477c7506ead6c_SA added
1477c73005d3cc_SAindex added
1477c72a457c40_sjdbInfo.txt added
1477c78edbd11_sjdbList.fromGTF.out.tab added
1477c793884f5_sjdbList.out.tab added
1477c76a2d3908_transcriptInfo.tab added
1477c72675cf5b_GRCh38.GENCODE.v42_100 added
1477c775ee3af6_knownGene_hg38.sql added
1477c716a393a3_knownGene_hg38.txt added
1477c7157e4a57_refGene_hg38.sql added
1477c7c0d542c_refGene_hg38.txt added
1477c756035c1e_knownGene_mm39.sql added
1477c7732e612f_knownGene_mm39.txt added
1477c76eb6450b_refGene_mm39.sql added
1477c73d045f26_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes

trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes

Data is downloaded: 
/tmp/Rtmpath6gg/test_gcpData/outfile.txt
}INFO Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added

Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]

[ FAIL 0 | WARN 1 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
> 
> 
> 
> proc.time()
   user  system elapsed 
 17.972   1.247  19.464